The Fiscal Calendar is stored in the Company Profile.

Note that you can run 'Close Year' for a range of departments rather than all of them. When Close Year is performed for a department, a flag is set to make sure you don't run it a second time. You can only run Close Year again if you happen to post another batch before running the Change Fiscal Year function.

Why are you trying to run Close Year twice? What this does is move balances from Income Statement accounts to Retained Earnings. Perhaps you have to make sure that you select only a particular department.